A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape

AbstractIn freshwater fish, processes of population divergence and speciation are often linked to the geomorphology of rivers and lakes that isolate populations. However, current geographical isolation does not necessarily imply total absence of gene flow during the divergence process. Here, we focused on four species of the genus Squalius in Portuguese rivers: S. carolitertii, S. pyrenaicus, S. aradensis and S. torgalensis. Previous studies based on eight nuclear and mitochondrial markers revealed incongruent patterns, with nuclear loci suggesting that S. pyrenaicus was a paraphyletic group since its northern populations were genetically closer to S. carolitertii than to its southern populations. For the first time, we successfully applied a genomic approach to the study of the relationship between these species, using a Genotyping by Sequencing (GBS) approach. Our results revealed a species tree with two main lineages: (i) S. carolitertii and S. pyrenaicus; (ii) S. torgalensis and S. aradensis. Regarding S. carolitertii and S. pyrenaicus, we found evidence for past introgression between the two in the northern part of S. pyrenaicus distribution. This introgression reconciles previous mitochondrial and nuclear incongruent results and explains the apparent paraphyly of S. pyrenaicus. Our demographic modelling estimates are consistent across models, suggesting that the northern populations of S. pyrenaicus received a contribution of approximately 90% from S. carolitertii and 10% from southern S. pyrenaicus. This illustrates that even in freshwater species currently allopatric, we are able to detect past gene flow events in present-day genomes, suggesting speciation is more complex than simply allopatric.

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A spatial genomic approach identifies time lags and historic barriers to gene flow in a rapidly fragmenting Appalachian landscape

10.1101/777920 ◽

2019 ◽

Author(s):

Thomas A. Maigret ◽

John J. Cox ◽

David W. Weisrock

Keyword(s):

Population Structure ◽

Gene Flow ◽

Genomic Data ◽

Data Sets ◽

Time Lags ◽

Genetic Structuring ◽

Data Set ◽

Landscape Modification ◽

Snp Data ◽

Genetic Patterns

AbstractThe resolution offered by genomic data sets coupled with recently developed spatially informed analyses are allowing researchers to quantify population structure at increasingly fine temporal and spatial scales. However, uncertainties regarding data set size and quality thresholds and the time scale at which barriers to gene flow become detectable have limited both empirical research and conservation measures. Here, we used restriction site associated DNA sequencing to generate a large SNP data set for the copperhead snake (Agkistrodon contortrix) and address the population genomic impacts of recent and widespread landscape modification across an approximately 1000 km2 region of eastern Kentucky. Nonspatial population-based assignment and clustering methods supported little to no population structure. However, using individual-based spatial autocorrelation approaches we found evidence for genetic structuring which closely follows the path of a historic highway which experienced high traffic volumes from ca. 1920 to 1970. We found no similar spatial genomic signatures associated with more recently constructed highways or surface mining activity, though a time lag effect may be responsible for the lack of any emergent spatial genetic patterns. Subsampling of our SNP data set suggested that similar results could be obtained with as few as 250 SNPs, and thresholds for missing data exhibited limited impacts on the spatial patterns we detected outside of very strict or permissive extremes. Our findings highlight the importance of temporal factors in landscape genetics approaches, and suggest the potential advantages of large genomic data sets and fine-scale, spatially-informed approaches for quantifying subtle genetic patterns in temporally complex landscapes.

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Arctic-adapted dogs emerged at the Pleistocene–Holocene transition

Science ◽

10.1126/science.aaz8599 ◽

2020 ◽

Vol 368 (6498) ◽

pp. 1495-1499 ◽

Cited By ~ 6

Author(s):

Mikkel-Holger S. Sinding ◽

Shyam Gopalakrishnan ◽

Jazmín Ramos-Madrigal ◽

Marc de Manuel ◽

Vladimir V. Pitulko ◽

...

Keyword(s):

Gene Flow ◽

Genetic Similarity ◽

Archaeological Evidence ◽

Origin And Evolution ◽

Sled Dogs ◽

Sled Dog ◽

Genomic Approach

Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog–specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.

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Genomic architecture controls spatial structuring in Amazonian birds

10.1101/2021.12.01.470789 ◽

2021 ◽

Author(s):

Gregory Thom ◽

Lucas Rocha Moreira ◽

Romina Batista ◽

Marcelo Gehara ◽

Alexandre Aleixo ◽

...

Keyword(s):

Gene Flow ◽

Life Histories ◽

Demographic History ◽

Bird Species ◽

Comparative Genomic ◽

Genomic Architecture ◽

Branching Model ◽

Whole Genomes ◽

Genomic Approach ◽

Neutral Models

Large rivers are ubiquitously invoked to explain the distributional limits and speciation of the Amazon Basin's mega-diversity. However, inferences on the spatial and temporal origins of Amazonian species have narrowly focused on evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known to produce heterogeneity in differentiation across the genome. To test how these factors may influence evolutionary inferences across multiple taxa, we sequenced whole genomes of populations for three bird species that co-occur in southeastern Amazonian and exhibit different life histories linked to their propensity to maintain gene flow across the landscape. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with the species tree topology weight. Gene flow was less pervasive in regions of low recombination, making these windows more suitable for commonly used phylogenetic methods that assume a bifurcating-branching model. To corroborate that these associations were attributable to selection, we modeled the signature of adaptive alleles across the genome taking demographic history into account, and found that on average 31.6 percent of the genome showed high probability for patterns consistent with selective sweeps and linked selection directly affecting the estimation of evolutionary parameters. By implementing a comparative genomic approach we were able to disentangle the effects of intrinsic genomic characteristics and selection from the neutral processes and show how speciation hypotheses are sensitive to genomic architecture.

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Matters of time (lags): Why we choose the lags we do, the difference it makes, and how we can make more informed choices

PsycEXTRA Dataset ◽

10.1037/e500122015-123 ◽

2014 ◽

Author(s):

James P. Selig

Keyword(s):

Time Lags ◽

The Difference

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Great Wall blocks gene flow

Nature ◽

10.1038/news030414-3 ◽

2003 ◽

Author(s):

HelenR. Pilcher

Keyword(s):

Gene Flow ◽

Great Wall

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Differentiation and Interrelations of Two Representatives of Laudakia stellio Complex (Reptilia: Agamidae) in Israel

Russian Journal of Herpetology ◽

10.30906/1026-2296-1997-4-2-102-114 ◽

2011 ◽

Vol 4 (2) ◽

pp. 102-114 ◽

Cited By ~ 2

Author(s):

Evgenyi N. Panov ◽

Larissa Yu. Zykova

Keyword(s):

Population Structure ◽

Gene Flow ◽

Habitat Preference ◽

Additional Data ◽

Near East ◽

Field Studies ◽

Subspecies Level ◽

Limited Gene Flow ◽

Study Sites ◽

And Behavior

Field studies were conducted in Central Negev within the breeding range of Laudakia stellio brachydactyla and in NE Israel (Qyriat Shemona) in the range of an unnamed form (tentatively “Near-East Rock Agama”), during March – May 1996. Additional data have been collected in Jerusalem at a distance of ca. 110 km from the first and about 170 km from the second study sites. A total of 63 individuals were caught and examined. The animals were marked and their subsequent movements were followed. Social and signal behavior of both forms were described and compared. Lizards from Negev and Qyriat Shemona differ from each other sharply in external morphology, habitat preference, population structure, and behavior. The differences obviously exceed the subspecies level. At the same time, the lizards from Jerusalem tend to be intermediate morphologically between those from both above-named localities, which permits admitting the existence of a limited gene flow between lizard populations of Negev and northern Israel. The lizards from NE Israel apparently do not belong to the nominate subspecies of L. stellio and should be regarded as one more subspecies within the species.

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